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Clinical Microbiology Reviews, July 2001, p. 547-560, Vol. 14, No. 3
0893-8512/01/$04.00+0   DOI: 10.1128/CMR.14.3.547-560.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

Alex van Belkum,1,* Marc Struelens,2 Arjan de Visser,3 Henri Verbrugh,1 and Michel Tibayrenc4

Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam,1 and Laboratory of Microbiology Wageningen Agricultural University, 6703 CT Wageningen,3 The Netherlands; Department of Microbiology Université Libre de Bruxelles Hôpital Erasme, Brussels, Belgium2; and Centre d'Etudes sur le Polymorphisme des Micro-Organismes, UMR CNRS/IRD 9926, Génétique Moléculaire des Parasites et des Vecteurs, IRD, 34032 Montpellier Cedex 1, France4

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.

* Corresponding author. Mailing address: Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center Rotterdam (EMCR), Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands. Phone: 31104635813. Fax: 31104633875. E-mail: vanbelkum{at}bacl.azr.nl.

Clinical Microbiology Reviews, July 2001, p. 547-560, Vol. 14, No. 3
0893-8512/01/$04.00+0   DOI: 10.1128/CMR.14.3.547-560.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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